# Protocol Commands Archive

Archived

This is for documentation only. The documentation for the latest version is available here.

# Available Commands v2.0036

Available Commands v2.0036

# _protocol_set_

Treating protocols as integrated sets.

Protocols are separate units which produce separate data sets. Using _protocol_set_, multiple protocols can be chained together into one protocol.

Note: This is different from chaining protocols together in a project. There, the protocols are still separate units within a measurement.

Input: array (opens new window)

Example:

"_protocol_set_": [
   { Protocol 1 },
   ...
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# adc_show

When "adc_show" is 1, the readings taken by the ADC (analog to digital converter) on the sample and hold circuit are outputted in "data_raw" instead of the normal output. No other output is recorded, and only the last set of adc readings is shown (all other readings are not outputted). By default there are 19 samples, but this can be changed using "number_samples".

Input: number (opens new window)

Values:

0, 1

Example:

"adc_show": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# autogain

The autogain function is added to the main section of the protocol. Multiple autogain functions can be run in a single protocol, and the indexed values should be useable throughout the experiment.

<index> which index to store gain settings (0-9)
<pulsed_LED> which pulsed LED to test (0-9)
<detector> which detector to use (0-3)
<pulse_duration> what duration to use (in microseconds) (1-200)
<target_value> what target value to use (0-65535, recommended: 40000-50000)

Input: nested array

Example:

"autogain": [
  [<index>, <pulsed_LED>, <detector>, <pulse_duration>, <target_value>],
  ...
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# averages

averages sets the number of times to average the protocol. The protocol will be repeated equal to the number of averages, and the resulting data will be averaged and outputted as a single data point. Averaging is often used to reduce noise and improve the quality of measurements.

Input: number (opens new window)

Values:

0 - 10000

Example:

"averages": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# averages_delay

averages_delay defines the delay between protocol averages in in milliseconds (ms).

Input: auto

Values:

0 - 9999999999

Example:

"averages_delay": <number>,

Dependencies:

averages

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# dac_lights

When dac_lights is set to 1, pulsed_lights_brightness and nonpulsed_lights_brightness settings will be interpreted by the device as 12-bit values (0 - 4095) directly controlling the LED voltage (via the DAC), instead of microEinsteins (µE * s⁻¹ * m⁻²). This is used during factory calibration.

Note: Setting brightness to high using raw DAC values could permanently disable LEDs, so be careful!

Input: number (opens new window)

Values:

0, 1

Example:

"dac_lights": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# detectors

detectors defines which detectors are being measured, and in what order. The chosen meas_light supplies the light source to be measured. The detector measurement is recorded in "data_raw" in the data received from the MultispeQ, which is then graphed for the user. When detectors is set to 0, no detector is read and responses will be recorded as zero.

Input: nested array

Values:

0 - 4

Example:

"detectors": [
  [ <detector> ],
  ...
],

Dependencies:

pulses
pulse_length
pulse_distance
pulsed_lights
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# energy_min_wake_time

The value of time is in milliseconds, and must be between zero and 10^6 milliseconds. This setting changes the delay between shutting off the 5V (following energy_save_timeout) and the wake up time. The energy_min_wake_time is needed to prevent brown out following the initiation of energy save.

Important: Note that the change in energy_min_wake_time will remain in effect until the instrument is reset, when it will return to the default value of 10 s.

Input: number (opens new window)

Values:

0 - 10^6

Example:

"energy_min_wake_time": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# energy_save_timeout

Adjusting Energy Save Timeout Time. The value of time is in milliseconds, and must be between zero and 10^6 milliseconds. This setting changes the energy_save_timeout time to prevent interference from the requirement for a 7 second wake up time from power save mode.

Important: Note that the change in energy_save_timeout will remain in effect until the instrument is reset, when it will return to the default value of 120 s.

Input: number (opens new window)

Values:

0 - 10^6

Example:

"energy_save_timeout": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# environmental

environmental defines which additional sensor(s) to measure. The environmental calls occur at the very beginning of the measurement, prior to any pulses. Some sensors require additional information, like specifying which pin to measure, brightness, etc. In addition to sensor measurements, there are also calls to flip digital pins on/off or set a pwm which could be used to control external lights or even motors. Below is the full list of parameters available in environmental.

. Adjusting protocols in real time based on these values can be very handy for certain types of protocols.

Input: nested array

Example:

"environmental": [
  [ <sensor> ],
  ...
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# environmental_array

environmental_array defines additional sensors or functionality, just like environmental. However, environmental_array returns sensor data once per pulse, as defined in pulses. This allows a string of sensor measurements to be used in a single macro. The advantage is you can calculate and return in real time things like rates of change, minima and maxima, etc. See examples for details. Note: pulsed_lights_brightness must NOT be set to zero for any given pulse set for the sensors set in environmental_array to measure.

Input: nested array

Example:

"environmental_array": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_length
pulse_distance
pulsed_lights
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# ir_baseline

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# label

Each protocol or sub-protocol can now output a label that can be used to indicate something about the protocol, conditions etc.

Input: string (opens new window)

Example:

"label": <string>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# max_hold_time

This parameter sets the time (in ms) at which the hold commands timeout. The default value is 15000, or 15 seconds. This value applies to the following control points: start_on_open, start_on_close, start_on_open_close.

Input: number (opens new window)

Example:

"max_hold_time": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# measurements

number of times to repeat a measurement, which is a set of protocols

Example:

"measurements": <number>

Last Updated: December 17, 2019

# measurements_delay

delay between measurements in milliseconds

Example:

"measurements_delay": <number>

Last Updated: December 17, 2019

# message

message sends text to the user between pulse sets, and waits for a response before proceeding. Set <message type> to "0" to not send a message. message should have the same length as pulses.

Input: nested array

Values:

alert - message with an OK button + prompt - message with an OK and Cancel button + confirm - message with an OK and Cancel button and text input box

Example:

"message": [
  [ <message type>, <message> ],
  ...
],

Dependencies:

pulses
pulse_length
pulse_distance

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# nonpulsed_lights

nonpulsed_lights defines which lights are not pulsed (always on) during a pulse set, and in what order.

Input: nested array

Values:

0 - 10

Example:

"nonpulsed_lights": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_distance
pulse_length
nonpulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# nonpulsed_lights_brightness

nonpulsed_lights_brightness sets the brightness in microEinsteins (µE * s⁻¹ * m⁻²) of the nonpulsed lights.

Input: nested array

Values:

0 - 15000

Example:

"nonpulsed_lights_brightness": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_distance
pulse_length
nonpulsed_lights

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# number_samples

number_samples sets the number of samples taken by the ADC (analog to digital converter) on the sample and hold circuit. The median value of these samples is then saved as a single detector value in "data_raw". The ADC is used to measure the detectors (1 - 4). This value is already set to the optimum value, and most signal noise comes from other source, but in certain cases increasing the value may yield improved signal.

Input: number (opens new window)

Values:

1 - 500

Example:

"number_samples": <number>,

Dependencies:

pulses
pulse_length
pulse_distance
detectors

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# open_close_start

When open_close_start is set to 1, the protocol waits until the user fully opens the clamp and closes the clamp before proceeding. Also works if the clamp starts fully open and then closes. Open and close is detected using the Hall effect sensor on the main body and magnet on the clamp (same sensor used to determine sample thickness). If the device is not calibrated, or calibration is off, or the clamping mechanism does not fully open or close, this function will not work. Calibration details can be found by typing print_memory into the console - see thickness_a, thickness_b, thickness_c, thickness_min, and thickness_max for relevant calibration values.

Input: number (opens new window)

Values:

0, 1

Example:

"open_close_start": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# par_led_start_on_close

The Ambient light is recreated inside the instrument on closing the clamp. During the hold time, the ambient light is resampled in ~100 ms intervals and the LED output is adjusted to match. When the hold event occurs (e.g. the clamp is closed), the final ambient intensity and LED setting are held and used in the protocol. The number for the LED is defining the LED used for matching the ambient light intensity.

Input: number (opens new window)

Example:

"par_led_start_on_close": <number for LED>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# par_led_start_on_open

The Ambient light is recreated inside the instrument on opening the clamp. During the hold time, the ambient light is resampled in ~100 ms intervals and the LED output is adjusted to match. When the hold event occurs (e.g. the clamp is closed), the final ambient intensity and LED setting are held and used in the protocol. The number for the LED is defining the LED used for matching the ambient light intensity.

Input: number (opens new window)

Example:

"par_led_start_on_open": <number for LED>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# par_led_start_on_open_close

Input: number (opens new window)

Example:

"par_led_start_on_open_close": <number for LED>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# protocols

protocols sets the number of times to repeat the protocol. Unlike averages, this outputs data every time the protocol is repeated (instead of averaging the repeats and outputting data only once).

Input: number (opens new window)

Values:

0 - 999999999

Example:

"protocols": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# protocols_delay

protocols_delay defines the delay between protocol repeats in in milliseconds (ms).

Input: auto

Values:

0 - 9999999999

Example:

"protocols_delay": <number>,

Dependencies:

protocols

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# pulse_distance

pulse_distance defines the distance, in microseconds (µs) between pulses.

Input: array (opens new window)

Values:

750 - 999999999999

Example:

"pulse_distance": [
  <number>,
  ...
],

Dependencies:

pulses
pulse_length
pulsed_lights
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# pulse_length

pulse_length defines the length, in microseconds (µs), of a pulse.

Input: nested array

Values:

1 - 150

Example:

"pulse_length": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_distance
pulsed_lights
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# pulsed_lights

pulsed_lights defines which lights are pulsed, and in what order. When set to 0, no lights are pulsed and no readings are recorded (see Example section here for details).

Input: nested array

Values:

0 - 10

Example:

"pulsed_lights": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_distance
pulse_length
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# pulsed_lights_brightness

pulsed_lights_brightness sets the brightness in microEinsteins (µE * s⁻¹ * m⁻²) of the pulsed lights.

Input: nested array

Values:

0 - 15000

Example:

"pulsed_lights_brightness": [
  [ <number> ],
  ...
],

Dependencies:

pulses
pulse_distance
pulse_length
pulsed_lights

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# pulses

pulses defines the number of pulse sets, and quantity of pulses per set.

Input: array (opens new window)

Values:

1 - 8000

Example:

"pulses": [
  <number>,
  ...
],

Dependencies:

pulse_distance
pulse_length
pulsed_lights
pulsed_lights_brightness

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# recall

This command returns values from the device memory (EEPROM). This includes values saved by the user (see Examples below for details) as well as values saved during factory calibration.

Input: array (opens new window)

Example:

"recall": [
  "userdef[<location>]",
  ...
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# reference

The MultispeQ is designed to be able to nearly simultaneously measure two detectors (within ~4µs), normalize and subtract the two signals from each other. This can be useful if there is a optical, electronic (interference), or LED (heating) artifact that needs to be removed. reference specifies another detector to be measured and subtracted from detectors.

Note: It is possible to add two additional detector circuits to the device, on the main body and clamp circuit boards. The devices come unpopulated by default. If added, these two additional detectors are available by settings detectors or reference to 2 (main body) or 4 (clamp). These can then also be used as reference or main detectors.

Input: nested array

Values:

1 - 4

Example:

"reference": [
  [ <detector> ],
  ...
],

Dependencies:

pulses
pulse_length
pulse_distance

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# save

This command saves a value to a location in the device memory (EEPROM).

Input: nested array

Example:

"save": [
  [ <location, <value> ],
  ...
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# save_trace_time_scale

Saving Time Scale Values. Setting the value to 0 will inactivate the function (preset), setting it to 1 will activate the function. If activated data_raw_time will be added to the measurement, containing the timing information.

Input: number (opens new window)

Values:

0 + 1

Example:

"save_trace_time_scale": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# set_led_delay

Pre-illuminating a sample. It is often useful to pre-illuminate a sample at a given light intensity, for a given amount of time.

Input: nested array

Example:

"set_led_delay": [
  [ <number LED>, <number duration in ms>, <number PAR> ],
  ...
],

// The following example gives two,
// 20 second pre-illuminations with the red LED (#2),
// the first at 0 µE * s⁻¹ * m⁻² and the second at 100 µE * s⁻¹ * m⁻²:

"set_led_delay": [
  [2, 20000,0],
  [2, 20000,100]
],

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# set_light_intensity

Instead of measuring the ambient light intensity, use set_light_intensity to set a fixed light intensity. Use the parameters light_intensity or previous_light_intensity to use the defined light intensity.

Note: Instead of defining the light intensity for each pulse set use set_light_intensity to only have one place to change the light intensity.

Input: number (opens new window)

Example:

"set_light_intensity": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# start_on_close

If set to 0, the command will be ignored. If set to 1, will wait until the clamp is closed, then proceed with the rest of the experiment.

Input: number (opens new window)

Values:

0 + 1

Example:

"start_on_close": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# start_on_open

If set to 0, the command will be ignored. If set to 1 or higher, it will wait until the clamp is opened, then proceed with the rest of the experiment.

Input: number (opens new window)

Values:

0 + 1

Example:

"start_on_open": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019

# start_on_open_close

If set to 0, the command will be ignored. If set to 1, will wait until the clamp is opened then closed, then proceed with the rest of the experiment.

Alias: open_close_start

Example:

"start_on_open_close": <number>,

Instruments:

MultispeQ 1 MultispeQ 2

Last Updated: December 17, 2019